Accepted alignment formats
CASP format
* Specify template: PARENT PDBCODE_CHAIN
* if no chain just use PDBCODE
Target seq Template seq
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Example of a CASP alignment
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PARENT 1ZIN
P 34 P 87
K 35 R 88
L 36 T 89
R 37 V 90
A 38 A 91
Q 39 Q 92
A 40 A 93
E 41 E 94
A 42 A 95
L 43 L 96
E 44 E 97
V 45 T 98
L 46 M 99
L 47 L 100
R 48 A 101
D 49 D 102
V 50 I 103
S 51 G 104
V 52 R 105
R 53 K 106
P 54 L 107
D 55 D 108
TER
END
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PIR
* target_name does not matter the parent is in "P1;PDBCODE_CHAIN"
* if no chain just use PDBCODE
* >P1; is important for identifying the alignment as PIR alignment.
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Example of a PIR alignment
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>P1;1ZIN
PRTVAQAEALETMLADIGRKLD*
>P1;target_name:
PKLRAQAEALEVLLRDVSVRPD*